\section*{Abbreviations}




\begin{acronym}[TDMA]
% \acro{CDMA}{Code Division Multiple Access}
% \acro{GSM}{Global System for Mobile communication}
% \acro{NA}[\ensuremath{N_{\mathrm A}}]
% {Number of Avogadro\acroextra{ (see \S\ref{Chem})}}
% \acro{NAD+}[NAD\textsuperscript{+}]{Nicotinamide Adenine Dinucleotide}
% \acro{NUA}{Not Used Acronym}
% \acro{TDMA}{Time Division Multiple Access}
% \acro{UA}{Used Acronym}
% \acro{lox}[\ensuremath{LOX}]{Liquid Oxygen}%
% \acro{lh2}[\ensuremath{LH_2}]{Liquid Hydrogen}%
\begin{singlespace}
\acro{1DE}{one-dimensional gel electrophoresis}
\acro{2DE}{two-dimensional gel electrophoresis} 
\acro{AGML}{Annotated Gel Markup Language}
\acro{BBSRC}{Biotechnology and Biological Sciences Research Council}




\acro{BFO}{Basic Formal Ontology}
\acro{ChEBI}{Chemical Entities of Biological Interest}

\acro{CISBAN}{Centre for Integrated Systems Biology of Ageing and Nutrition}


\acro{CV}{Controled vocabulary}
\acro{CS}{New Born Calf Serum}
\acro{CY}{cytosol} 
\acro{DOC}{Deoxycholic acid}
\acro{DOLCE}{Descriptive Ontology for Linguistic and Cognitive Engineering}

\acro{DIGE}{difference gel electrophoresis}
\acro{DMEM}{Dulbecco's Modified Eagle Medium}
\acro{DTT}{dithiothreitol}  

\acro{EDTA}{ethylene diamine tetraacetic acid}

\acro{ESI}{electrospray ionisation}


\acro{FBS}{Foetal bovine serum}
\acro{FFAs}{free fatty acids}
\acro{FG}{functional genomics}
\acro{FuGE}{Functional Genomics Experiment} 

\acro{FRET}{fluorescent resonance energy transfer}
\acro{FT}{Fourier transform}  

\acro{G3P}{Glycerol-3-phosphate}

\acro{GAP}{GTPase Activating Protein}
\acro{GELI}{Gel Electrophoresis Information}

\acro{GELI-ML}{GELI markup language}
\acro{GelInfoML}{Gel electrophoresis informatics markup language}
\acro{GelML}{Gel Electrophoresis Markup Language} 

\acro{Gel WG}{The Proteomics Standards Initiative Gel based analysis working group}
\acro{GLUT}{glucose transporters}
\acro{GLUT4}{glucose transporter 4}

\acro{GO}{Gene Ontology}
\acro{GOLD}{Genomes OnLine Database}
\acro{GSV}{GLUT4 storage vesicle}
\acro{HEPES}{4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid}

\acro{HES}{\ac{HEPES}, \ac{EDTA}, Sucrose}

\acro{HDM}{high density microsome} 
 
\acro{HRP}{horseradish peroxidase}

\acro{HUP-ML}{Human Proteome Markup Language}

\acro{HUPO}{Human Proteome Organisation}

\acro{ICR}{ion cyclotron resonance}


\acro{JHUPO}{Japanese Human Proteome Organisation}
\acro{kDa}{Kilo dalton}
\acro{IAA}{iodoacetamide}
\acro{ICAT}{isotope-coded affinity tags}
\acro{IBMX}{methyl isobutylxanthine}
\acro{IPG}{immobilised pH gradient}

\acro{IR}{insulin receptor}
\acro{IRS}{insulin receptor substrate}

\acro{LC}{liquid chromatography}
\acro{LDM}{low density microsome} 
\acro{LDS}{lithium dodecyl sulfate}
\acro{LIMS}{Laboratory Information Management System}
\acro{MAGE-ML}{Microarray Gene Expression markup language}

\acro{MALDI}{matrix-assisted laser desorption/ionization}

\acro{MSI}{Metabolomics Standards Initiative}

\acro{MGED}{Microarray Gene Expression Data Society}

\acro{MIAPE}{Minimum Information About a Proteomics Experiment}

\acro{MIAPE GE}{Minimum Information About a Proteomics Experiment: Gel Electrophoresis}
\acro{MIAPE GI}{Minimum Information About a Proteomics Experiment: Gel Informatics}

\acro{MIAME}{Minimum Information About a Microarray Experiment}

\acro{MIBBI}{Minimum Information for Biological and Biomedical Investigations}

\acro{M/N}{mitochondria and nuclei}


\acro{MS}{Mass Spectrometry}

\acro{MW}{molecular weight}
\acro{mz}[\ensuremath{\textit{m/z}}]{mass to charge ratio}

\acro{NMR}{nuclear magnetic resonance}

\acro{OBO}{Open Biomedical Ontology}

\acro{OBO-format}{Open Biomedical Ontology format}

\acro{OBI}{Ontology of Biomedical Investigations}

\acro{OPD}{Open Proteomics Database}

\acro{OWL}{Web Ontology Language}

\acro{PATO}{Phenotypic quality ontology}
\acro{PBS}{Dulbecco's Phosphate Buffered Saline}
\acro{PDF}{Portable Document Format}
\acro{PDI}{Protein disulfide-isomerase}
\acro{PEDRo}{Proteomics Experiment Data Repository}

\acro{pI}{iso-electric point}

\acro{PH}{pleckstrin homology}

\acro{PI}{phosphoinositide}
\acro{PI3K}{phosphatidylinositol 3-kinase}
\acro{PIP3}[PIP\ensuremath{_3}]{phoshpatidylinositol-3,4,5-triphosphate}
\acro{PDK-1}{3 phosphoinositidedependent kinase-1}
\acro{PDK-2}{3 phosphoinositidedependent kinase-2}
\acro{PKB}{protein kinase B}

\acro{PM}{plasma membrane}
\acro{PMF}{peptide mass fingerprint}
\acro{PBMS}{Probability Based Mowse Score}


\acro{PMSF}{phenylmethylsulphonyl fluoride}

	
\acro{PRIDE}{Proteomics Identifications Database}

\acro{PS}{Penicillin Streptomycin}
\acro{PSI}{Proteomics Standards Initiative}
\acro{PVDF}{Polyvinylidene fluoride}
\acro{RSBI}{Reporting Structure for Biological Investigations}


\acro{RDF}{Resource Description Framework}
\acro{RO}{Relations Ontology}
\acro{RU}{representational unit}

\acro{sepCV}{Sample processing and separation techniques Controlled Vocabulary}
\acro{SDS}{sodium dodecyl sulphate}
\acro{SDS-PAGE}{sodium dodecyl sulphate polyacrylamide gel electrophoresis}

\acro{SH2}{Src Homology 2}

\acro{SILAC}{stable isotope labeling by amino acids in cell culture}



\acro{spML}{sample processing Markup language}
\acro{SUMO}{Suggested Upper Merged Ontology}
\acro{TCA}{tricarboxylic acid}
\acro{TIFF}{Tagged Image File Format}
\acro{TOF}{time of flight}

\acro{TNF}[{TNF-$\alpha$}]{tumour necrosis factor-alpha} %ensuremath
\acro{TTBS}{Tween-Tris Buffered Saline}
\acro{TBS}{Tris Buffered Saline}
\acro{UML}{Unified Modeling Language}

\acro{URI}{Uniform Resource Identifier}

\acro{UO}{Unit ontology}
\acro{UV}{ultra violet}

\acro{W3C}{World Wide Web Consortium}
\acro{WHO}{World heath organisation}
\acro{WG}{working group}

\acro{XML}{Extensible Markup Language}
\end{singlespace}
\end{acronym}

